Interesting.
During this process, I found that there were 5 or 6 empty sockets (regular bulbs, not flashers) on the back board, mostly behind Data's head. I put new bulbs in there, and they now light up fine.
Now I'm getting a ball cycling, I assumed it was a problem with the opto board in the trough, but it could be caused by the diverter coil cycling.
A few days before all the trouble, I also had to replace one of the diverter coils in the subway- now I'm assuming that it may all be related? The coil melted the sleeve, I (probably incorrectly) figured that the coil was just bad.
Maybe I do have a weird short somewhere????
Honestly, I don't think I'll turn it on again, JR from Pinball Plus is coming to take a look.